In spite of the extensive amount of research and characterization which has characterized modern biology, only a small portion of the world's microbial species have yet been identified and characterized. In particular, it is well known that the rain forest regions of the planet contain an enormous diversity of flora and fauna including many species which have not yet been recognized by science. Not only have the diversity of life forms at a macrobiological scale been only partly characterized by modern science, very little work has been done in examining the microbiological diversity of the rain forest ecosystems.
The Amazon Basin of South America is the largest tropical rain forest on the planet. There have been estimates that there may be as many as thirty million species of tropical forest arthropods, an estimate which exemplifies the immense biodiversity found in the Amazon Basin. The microbial diversity of the Amazon remains largely uncharacterized. There are numerous factors which lead to this deficiency, not the least of which is the inability of science at present to culture many microorganisms. In soil, comparisons of microbial cell numbers by microscopic counts and enumeration on culture media have shown that using conventional media less than 1% of the native microorganisms can be cultivated. The quantification of this uncharacterized diversity in soils has suggested some startling results.
By measuring the kinetics of denaturation and renaturation of bacteria DNA extracted from soil, one group of scientists have been able to estimate that there are at least 400 different genomes of bacteria contained in a single gram of soil taken from a Norwegian forest. The understanding of the diversity of this microbiological community is thus clearly limited given our present understanding. To address this issue, recent reports have shown that PCR amplification and sequence analysis of rRNA genes can help to provide a phylogenic description of the microorganisms that inhabit the soil.
Ribosomal RNA genes (rDNA) are used to characterize the phylogenic classification of microorganisms. rDNA sequences are used since these particular DNA sequences tend to be highly conserved among closely related organisms. rRNAs or rDNAs are characterized at present as the most useful and most used of the molecular chronometers. By chronometers it is meant to describe a molecule which changes randomly in time and therefore can be used to judge the relatedness of different organisms. The difference in sequence between the rRNA or the rDNA of particular organisms is recognized as a measure of the time at which the two organisms diverged on an evolutionary scale. The use of rRNA sequences as a measurement of molecular chronometer and as a tool for analyzing the phylogenic tree of microorganisms is described in a review article by Woese, Microbiol. Rev. 51,2:221-271 (1987), the disclosure of which is hereby incorporated by reference. Within the general realm of ribosomal RNA, a particular portion which has been utilized for phylogenic characterization is the 16S-like rRNA sequences. An early phylogenic tree of the major classifications of life is illustrated by Pace, et al., Journal Cell, 45:325-326 (1986).